LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
units           real
atom_style      full
boundary        p p p
dielectric      1
special_bonds   lj/coul 0.0 0.0 1.0

pair_style      hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000  11.5
bond_style      harmonic
angle_style     harmonic
dihedral_style  harmonic
improper_style  none
kspace_style    pppm 0.001

read_data       data.dreiding
  orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
  2 by 1 by 2 MPI processor grid
  reading atoms ...
  384 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  3 = max dihedrals/atom
  reading bonds ...
  320 bonds
  reading angles ...
  448 angles
  reading dihedrals ...
  192 dihedrals
  4 = max # of 1-2 neighbors
  3 = max # of 1-3 neighbors
  5 = max # of special neighbors

pair_coeff      1    1    lj/cut/coul/long        0.015200000256300         2.846421344984478
pair_coeff      1    2    lj/cut/coul/long        0.001232882795416         2.846421344984478
pair_coeff      1    3    lj/cut/coul/long        0.038019995160237         3.159705878878677
pair_coeff      1    4    lj/cut/coul/long        0.038139744011598         2.939787518071103
pair_coeff      2    2    lj/cut/coul/long     9.99999974737875e-05         2.846421344984478
pair_coeff      2    3    lj/cut/coul/long        0.003083828758188         3.159705878878677
pair_coeff      2    4    lj/cut/coul/long        0.003093541672406         2.939787518071103
pair_coeff      3    3    lj/cut/coul/long        0.095100000500679         3.472990412772877
pair_coeff      3    4    lj/cut/coul/long        0.095399530150179         3.253072051965302
pair_coeff      4    4    lj/cut/coul/long        0.095700003206730         3.033153691157727
pair_coeff      4    4    hbond/dreiding/lj  2  i  4.000    2.750000000000000      4
pair_modify     mix arithmetic
neighbor        2.0 multi
neigh_modify    every 2 delay 4 check yes
variable        input index in.ch3oh.box.dreiding
variable        sname index ch3oh.box.dreiding

compute   hb all pair hbond/dreiding/lj
variable    C_hbond equal c_hb[1] #number hbonds
variable    E_hbond equal c_hb[2] #hbond energy
thermo_style    custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
thermo_modify   line multi format float %14.6f

fix      1      all nve

thermo 10

run 100
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00064 (src/kspace.cpp:302)
  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
  G vector (1/distance) = 0.142073
  grid = 3 3 3
  stencil order = 5
  estimated absolute RMS force accuracy = 0.154715
  estimated relative force accuracy = 0.00046592
  using double precision FFTs
  3d grid and FFT values/proc = 392 12
Neighbor list info ...
  update every 2 steps, delay 4 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 13.5
  ghost atom cutoff = 13.5
  binsize = 6.75, bins = 3 3 3
  3 neighbor lists, perpetual/occasional/extra = 3 0 0
  (1) pair hbond/dreiding/lj, perpetual, skip from (3)
      attributes: full, newton on
      pair build: skip
      stencil: none
      bin: none
  (2) pair lj/cut/coul/long, perpetual, half/full from (3)
      attributes: half, newton on
      pair build: halffull/newton
      stencil: none
      bin: none
  (3) neighbor class addition, perpetual
      attributes: full, newton on
      pair build: full/multi
      stencil: full/multi/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.17 | 10.17 | 10.17 Mbytes
---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
TotEng   =     113.723601 KinEng   =       0.000000 Temp     =       0.000000 
PotEng   =     113.723601 E_bond   =       0.535673 E_angle  =       1.281880 
E_dihed  =       1.232497 E_impro  =       0.000000 E_vdwl   =    -125.381324 
E_coul   =     597.219740 E_long   =    -361.164864 v_E_hbond =     -69.322152 
v_C_hbond =     235.000000 Press    =    -328.847347 Volume   =    7447.236335 
---------------- Step       10 ----- CPU =      0.0112 (sec) ----------------
TotEng   =     113.773202 KinEng   =       1.537257 Temp     =       1.346522 
PotEng   =     112.235945 E_bond   =       0.530880 E_angle  =       1.407481 
E_dihed  =       1.084172 E_impro  =       0.000000 E_vdwl   =    -126.339883 
E_coul   =     596.742306 E_long   =    -361.189011 v_E_hbond =     -69.944278 
v_C_hbond =     240.000000 Press    =    -395.900496 Volume   =    7447.236335 
---------------- Step       20 ----- CPU =      0.0206 (sec) ----------------
TotEng   =     113.879292 KinEng   =       2.999580 Temp     =       2.627407 
PotEng   =     110.879711 E_bond   =       0.549156 E_angle  =       1.323582 
E_dihed  =       1.357398 E_impro  =       0.000000 E_vdwl   =    -127.482103 
E_coul   =     596.318729 E_long   =    -361.187051 v_E_hbond =     -70.088343 
v_C_hbond =     237.000000 Press    =    -487.150418 Volume   =    7447.236335 
---------------- Step       30 ----- CPU =      0.0299 (sec) ----------------
TotEng   =     113.587474 KinEng   =       4.369566 Temp     =       3.827412 
PotEng   =     109.217908 E_bond   =       0.416485 E_angle  =       1.294630 
E_dihed  =       1.710254 E_impro  =       0.000000 E_vdwl   =    -128.565697 
E_coul   =     595.560846 E_long   =    -361.198612 v_E_hbond =     -69.848068 
v_C_hbond =     238.000000 Press    =    -423.966898 Volume   =    7447.236335 
---------------- Step       40 ----- CPU =      0.0403 (sec) ----------------
TotEng   =     113.915503 KinEng   =       6.466349 Temp     =       5.664037 
PotEng   =     107.449154 E_bond   =       0.514530 E_angle  =       1.342583 
E_dihed  =       1.536929 E_impro  =       0.000000 E_vdwl   =    -129.858713 
E_coul   =     595.186400 E_long   =    -361.272576 v_E_hbond =     -69.871393 
v_C_hbond =     237.000000 Press    =    -498.152652 Volume   =    7447.236335 
---------------- Step       50 ----- CPU =      0.0494 (sec) ----------------
TotEng   =     113.787839 KinEng   =       8.050614 Temp     =       7.051734 
PotEng   =     105.737226 E_bond   =       0.652153 E_angle  =       1.416041 
E_dihed  =       1.363560 E_impro  =       0.000000 E_vdwl   =    -130.513518 
E_coul   =     594.139769 E_long   =    -361.320780 v_E_hbond =     -69.593967 
v_C_hbond =     233.000000 Press    =    -557.299799 Volume   =    7447.236335 
---------------- Step       60 ----- CPU =      0.0588 (sec) ----------------
TotEng   =     114.120941 KinEng   =      10.318793 Temp     =       9.038489 
PotEng   =     103.802148 E_bond   =       0.576578 E_angle  =       1.285008 
E_dihed  =       1.123936 E_impro  =       0.000000 E_vdwl   =    -131.268312 
E_coul   =     593.450009 E_long   =    -361.365070 v_E_hbond =     -70.107165 
v_C_hbond =     238.000000 Press    =    -571.907188 Volume   =    7447.236335 
---------------- Step       70 ----- CPU =      0.0680 (sec) ----------------
TotEng   =     113.836161 KinEng   =      11.873184 Temp     =      10.400019 
PotEng   =     101.962977 E_bond   =       0.633521 E_angle  =       1.315999 
E_dihed  =       1.055318 E_impro  =       0.000000 E_vdwl   =    -131.673572 
E_coul   =     592.039194 E_long   =    -361.407483 v_E_hbond =     -70.518544 
v_C_hbond =     240.000000 Press    =    -576.731444 Volume   =    7447.236335 
---------------- Step       80 ----- CPU =      0.0790 (sec) ----------------
TotEng   =     113.589436 KinEng   =      13.546467 Temp     =      11.865689 
PotEng   =     100.042970 E_bond   =       0.637759 E_angle  =       1.439918 
E_dihed  =       1.020307 E_impro  =       0.000000 E_vdwl   =    -131.980346 
E_coul   =     590.365879 E_long   =    -361.440548 v_E_hbond =     -71.174370 
v_C_hbond =     245.000000 Press    =    -735.254308 Volume   =    7447.236335 
---------------- Step       90 ----- CPU =      0.0883 (sec) ----------------
TotEng   =     114.100567 KinEng   =      15.870735 Temp     =      13.901574 
PotEng   =      98.229832 E_bond   =       0.724671 E_angle  =       1.435914 
E_dihed  =       1.028167 E_impro  =       0.000000 E_vdwl   =    -132.680267 
E_coul   =     589.225626 E_long   =    -361.504279 v_E_hbond =     -72.653223 
v_C_hbond =     245.000000 Press    =    -820.598954 Volume   =    7447.236335 
---------------- Step      100 ----- CPU =      0.0976 (sec) ----------------
TotEng   =     113.670041 KinEng   =      17.406803 Temp     =      15.247054 
PotEng   =      96.263238 E_bond   =       0.711253 E_angle  =       1.338059 
E_dihed  =       1.474770 E_impro  =       0.000000 E_vdwl   =    -132.917719 
E_coul   =     587.219020 E_long   =    -361.562145 v_E_hbond =     -74.299795 
v_C_hbond =     246.000000 Press    =    -786.245946 Volume   =    7447.236335 
Loop time of 0.0976357 on 4 procs for 100 steps with 384 atoms

Performance: 88.492 ns/day, 0.271 hours/ns, 1024.215 timesteps/s
96.1% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.055383   | 0.065178   | 0.07438    |   2.7 | 66.76
Bond    | 0.00099874 | 0.0011503  | 0.001229   |   0.3 |  1.18
Kspace  | 0.013823   | 0.022918   | 0.032308   |   4.4 | 23.47
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0064669  | 0.0072899  | 0.0078194  |   0.6 |  7.47
Output  | 0.00039268 | 0.00043893 | 0.00056481 |   0.0 |  0.45
Modify  | 0.000175   | 0.00019002 | 0.00020623 |   0.0 |  0.19
Other   |            | 0.0004706  |            |       |  0.48

Nlocal:    96 ave 104 max 87 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost:    3063.25 ave 3108 max 3024 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs:    25463.5 ave 28799 max 22471 min
Histogram: 1 0 0 1 0 1 0 0 0 1
FullNghs:  1406 ave 1664 max 1237 min
Histogram: 1 0 1 1 0 0 0 0 0 1

Total # of neighbors = 101854
Ave neighs/atom = 265.245
Ave special neighs/atom = 4
Neighbor list builds = 0
Dangerous builds = 0

Please see the log.cite file for references relevant to this simulation

Total wall time: 0:00:00
